Entering edit mode
4.7 years ago
Sadik Muzemil
▴
20
Hello there,
I am using Platanus-allee 2.2.2 to generate hybrid assembly of Illumina short reads and PacBio reads. I have got contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours
Error(13): Error, SolveDBG exception!! platanus_allee solve_DBG command failed.
Here is the script used for contig assembly and phasing
num_threads=20
tmp_dir=/path-to-/tem/platanus_allee
memory_GB=100
out_prefix=out
minimap2_path=minimap2
# Input reads
PE=trimmed_L1_*.fq
PacBio=pacbio*.fastq.gz
# Contig assembly commands
platanus_allee assemble -t ${num_threads} -tmp ${tmp_dir} -m ${memory_GB} -o ${out_prefix} \
-f $PE \
2>${out_prefix}.assembleLog
# phasing commands
platanus_allee phase -t ${num_threads} -tmp ${tmp_dir} -o ${out_prefix} -mapper ${minimap2_path} \
-c out_contig.fa \
-IP1 $PE -p $PacBio \
2>${out_prefix}.phaseLog
cat out.phaseLog
platanus_allee version: 2.2.2
platanus_allee phase -t 20 -tmp /path-to-/tem/platanus_allee -o out -mapper minimap2 -c out_contig.fa -IP1 trimmed_L1_1.fq trimmed_L1_2.fq -p /path-to-/pacbio*.fastq.gz
Error(13): Error, SolveDBG exception!!
platanus_allee solve_DBG command failed.
tail -n 15 path-to-/out_intermediateResults/round1/out.solveDBGLog
dividing nodes based on bubbles ...
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 1832
dividing scaffolds to adjust bubble-breakpoints...
dividing indonsistent bubble-ends...
pairing bubble nodes...
dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
NUM_DIVISION = 0
TOTAL_NUM_DIVISIONS =1832
dividing erroneous scaffolds based on base-level coverages ...
Segmentation fault (core dumped)
A bug causing the segmentation fault seems issue on Platanus-allee v2.0.0 and earlier
Any suggestion please?
I'm running into the same issue - platanus_allee assemble worked, but I get the error code when running the phasing command.
Did you end up finding a solution?
Hi, I did not find a way to work it out and finally gave up on it and switched to my focus to SPAdes.
Hello, I am also getting the same error using the 2.2.2 version. Also wrote to the authors but no answer. Did anybody found a solution? The original paper has been cited 25 times (according to WOS) so I assume this error is not a bug?